NM_007109.3:c.*1213T>C

Variant names:

• chr6-31163930-T-C
• rs9501062
• NM_007109.3:c.*1213T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007109.3(TCF19):​c.*1213T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 985,596 control chromosomes in the GnomAD database, including 994 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.064 (508 hom., cov: 32)
  • Exomes 𝑓: 0.027 (486 hom.)
• Consequence: TCF19 NM_007109.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 9 publications found

Genes affected

TCF19 (HGNC:11629): (transcription factor 19) This gene encodes a protein that contains a PHD-type zinc finger domain and likely functions as a transcription factor. The encoded protein plays a role proliferation and apoptosis of pancreatic beta cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCF19	NM_007109.3	c.*1213T>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000376257.8	NP_009040.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCF19	ENST00000376257.8	c.*1213T>C		3_prime_UTR_variant	Exon 4 of 4	1	NM_007109.3	ENSP00000365433.3

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9696 AN: 151916 Hom.: 506 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0339

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0419

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0241

Gnomad OTH AF: 0.0636

GnomAD4 exome AF: 0.0271 AC: 22623 AN: 833562 Hom.: 486 Cov.: 32 AF XY: 0.0270 AC XY: 10384 AN XY: 384958

African (AFR) AF: 0.138 AC: 2184 AN: 15788

American (AMR) AF: 0.0400 AC: 42 AN: 1050

Ashkenazi Jewish (ASJ) AF: 0.0285 AC: 147 AN: 5160

East Asian (EAS) AF: 0.165 AC: 601 AN: 3638

South Asian (SAS) AF: 0.0341 AC: 562 AN: 16476

European-Finnish (FIN) AF: 0.0504 AC: 14 AN: 278

Middle Eastern (MID) AF: 0.0321 AC: 52 AN: 1622

European-Non Finnish (NFE) AF: 0.0234 AC: 17803 AN: 762242

Other (OTH) AF: 0.0446 AC: 1218 AN: 27308

GnomAD4 genome AF: 0.0638 AC: 9700 AN: 152034 Hom.: 508 Cov.: 32 AF XY: 0.0651 AC XY: 4837 AN XY: 74328

African (AFR) AF: 0.137 AC: 5667 AN: 41430

American (AMR) AF: 0.0338 AC: 517 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3470

East Asian (EAS) AF: 0.167 AC: 861 AN: 5162

South Asian (SAS) AF: 0.0419 AC: 202 AN: 4820

European-Finnish (FIN) AF: 0.0528 AC: 558 AN: 10568

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0241 AC: 1641 AN: 67976

Other (OTH) AF: 0.0643 AC: 136 AN: 2114

Alfa AF: 0.0393 Hom.: 916

Bravo AF: 0.0672

Asia WGS AF: 0.113 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.0
DANN	Benign	0.76
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9501062; hg19: chr6-31131707;